Project Analysis update news
- 12 July 2007««
• The management of the J2 Y-DNA project has changed. The J2 Y-DNA project is now managed by myself Angela Cone (previously co-admin). I'd like to reassure everyone that this change in management will not affect the quality of the J2 Y-DNA projects Scientific research in any way.
You'll see that the new project website has had a facelift, but overall retains much the same content as the old site. Over the next few months, the phase two and phase three analyses will be repeated and new content will be added to the site (eg. the taxonomy pages will be expanded).
A few months ago, Costa. and I agreed that we would make the publicly viewable project pages more accessible. This previously planned change has now been made - you'll see that the project copyright has now been replaced with a creative commons licence. You can now copy/print the public project pages (just do so in accordance with the creative commons licence). We also discussed future changes like making .pdf downloads of project analysis results available - and these changes will be implemented once the phase two and three analyses have been repeated.
An addition I'm adding to the project is the establishment of a group fund for the J2 Y-DNA project, to be used to help pay for high priority testing. I've started the "ball rolling" by making a donation to the group fund. See here for more details.
Finally, I sincerely thank Costa. Tsirigakis for founding the J2-YDNA project, and providing such a solid scientific, ethical foundation for the project.
• J2b-Delta cluster research update.
[originally written July 1st 2008]
Now that FTDNA is testing for M241 (as well as other new SNPS), we are getting some new M241 results.
In February we concluded that most J2b M205- haplotypes are probably M241+ (with perhaps just J2b-Gamma cluster haplotypes the exception). Well,.. it appears that we were wrong...
I am currently aware of three haplotypes that have tested as J2b* (ie. M205-, M241-). The placement of these three haplotypes in the J2b haplotype clustering is indicated in the diagram below (along with the placement of M241 haplotypes, and the haplotypes which currently have M241 tests pending).
As can be seen, J2b* haplotypes have so far been found in both J2b-Delta and J2b-Alpha. We can also see that J2b2 haplotypes (J M241+) have been found in J2b-Alpha, J2b-Delta, J2b-Gamma and J2b-Zita clusters (but not J2b-Beta cluster). On the other hand J2b1 (M205+) haplotypes are confined to J2b-Beta cluster.
From this information we have (which is still a relatively low sample size) we might conclude that there is convergence in the clustering of J2b* and J2b2 haplotypes (yet both are easily distinguishable from J2b1), or testing error has occurred (ie. the J2b* haplotypes might really be M241+).
Over the last year, the J2 Y-DNA project has emphasized that haplotype clusters are not the same as haplogroup clades. In some cases haplotypes may cluster together due to a true biological relationship, but other times haplotypes may cluster together due to haplotype convergence. If I see a discrepancy between haplotype clustering and SNP results, my first tendancy is to assume that convergence has occurred (and that the SNP result is accurate).
The projects original hypotheses regarding J2a-Delta cluster can be seen here, and updates can be seen here (April 2007) and here (February 2008).
If these new results are genuine (ie. there really are two M241- haplotypes in J2b-Delta cluster) then what does this mean in terms of the projects hypotheses about J2b-Delta cluster? - well at this stage it's too early to tell.
To find out whether these new results do falsify the J2b-Delta hypotheses, we need more J2b-Delta haplotypes tested for M241. Currently there are eight members waiting to receive M241 results. Three of these members are in J2a-Delta (two of which are likely related in a genealogical time frame). In addition, three of these nine members have previously tested positive for M241 at another lab (one of which is in J2b-Delta). Therefore, we'll also have an extra level of result accuracy verification (ie. we'll be able to exclude lab error as a cause for these J2b* results).
In about 6-8 weeks time (after those results have arrived), I will issue an update regarding the J2b-Delta hypotheses. At the moment I am inclined to think that these new results will "blow the J2a-Delta hypotheses out of the water" (ie. falsify them) - but who knows, we may be surprised!
Future developments will be very very interesting to see...
[update - 7 July 08] M241 test results have arrived back for two of the members who had M241 tested previously. For both members, the results from the different DNA companies agreed (M241+). One of these members is in J2b-Delta cluster, and the other in J2b-Alpha cluster.
[update - 11 July 08] An additional M241+ result has arrived for a member in J2b-Alpha cluster.
• We now have three members in J2b-Zita with DYS413 tested. In February we reported that a J2b-Zita member with a GD of 18/37 (from the member who has DYS413 values of 18, 23) received results of 21 23. Since then we have had a member with a GD of 6/37, who has also received results of 21 23. At this stage it seems likely that the one example of a J2b haplotype with DYS413 values of 18 23 represents a private mutation.
I thank those of you in J2b-Zita who tested DYS413.
- 3 April 2007««
• The New YCC tree has now been published. It is contained in a research paper (Karafet et al. 2008) in the Scientific Journal "Genome research". Details of this new tree can be seen on the projects nomenclature page found here. To assist all, we have included a diagram which shows the new nomenclature with the old nomenclature labels alongside.
We will be updating all the project websites pages (including results tables) over the next couple of days to incorporate the new nomenclature.
- 15 February 2008««
Part two of the "October 2007" update
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The new public results haplotype table has been added to the project website. This results table contains the haplotypes of members who have specifically given their informed consent. Of those members who responded, about 2/3 gave their full consent, and about 1/3 consented only to having their haplotype in the members area (not in the public area).
This results table will be manually updated with new results on a monthly basis (unfortunately it cannot be automatically updated). It will next be updated in the second week of March 2008. |
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The member map on the public results page has been updated. This new version of the map shows members who have SNP test results in grey, blue and red. For the remainder of haplotypes (ie. those that do not have sub-clade results) we have predicted whether they are likely to be J2 M410+ or J2 M12+ (white or pale reddish). |
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Additional information about J2b, J2a-Beta (and J2b-Lambda & J2a-Theta) has been added to the phase three cluster analysis page. This includes distribution maps of the clusters mentioned. We also add some information about J (xM12) haplotypes that have DYS 413 >18.
In this section we also update our investigation into J2b-Delta and its distribution (especially in relation to the British Isles). A year ago, we first examined the apparent association between J2b-Delta and the British Isles. We hypothesized that J2b-Delta might represent a genuine clade, and that we'd need to find a corresponding SNP marker to confirm this hypothesis.
Preliminary results indicate that If there is a SNP that defines J2b-Delta and/or J2b-Zita from J2b-Alpha (or vice versa) then it is not M241. So far, all non J2b-Beta haplotypes that have tested for M241 have received a result of "derived" (ie. positive). The project has yet to see a J2b haplotype confirmed to be negative for both M241 and M205. If there are any M241/M205 negative haplotypes in the project, then the most likely candidates are probably the haplotypes that are currently categorised in J2b-Gamma. However, - it is important to remember that this is only a hypothesis that can only be confirmed with additional testing. |
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A new "hypotheses" page has been added, which outlines questions/hypotheses that have been generated by the J2 Y-DNA projects research. We are hoping that FTDNA's new "walk on the Y" can help answer some of these questions (as well as the continued research by Ethnoancestry). |
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The new YCC tree has not yet been published. We were hoping to upload this update to the site just after the release of the YCC tree - but we have waited far too long now. We currently have our haplotype table results in the FTDNA 2005 nomenclature, and will update our pages to the new YCC nomenclature when the paper is published.
Please note that the forthcoming new tree will be an update of the official YCC NRY phylogenetic tree, that scientists will subsequently use in scientifically legitimate publications.
This tree is being published in a scientific journal, so the delay is likely to be the result of normal delays (eg. peer review) that do occur when scientific research is published . |
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The J2 Y-DNA project was very interested to hear about Ethnoancestry's discovery of a new SNP marker, "S57" which may be more-or-less equivalent to the DYS 413 deletion.
Back in October 2007, The project presented a review that documented why STR's (and DYS 413 especially) cannot be used in the YCC's binomial NRY Phylogenetic tree. In that analysis, we concluded that STR markers like DYS 413 are definitely extremely useful, valuable and informative, but however useful, valuable and informative they are - they cannot be used as a taxonomic character in the binomial NRY phylogenetic tree (since the tree is binomial as defined by the YCC, and STR markers are not binomial characters). For more information see these pages:
(especially those marked by **)
• J2 Nomenclature page
• The DYS 413 review page **
• Menu for the taxonomy pages
• Taxonomy basics
• YCC Nomenclature
• Cladistics **
Therefore, it is very exciting that a new SNP has been found that may be equivalent to the primary DYS 413 deletion - and may therefore offer a far more reliable alternative to DYS 413 that can in time be included in the official scientific YCC NRY phylogenetic tree. Unfortunately though, this new SNP was not discovered in time for inclusion in the forthcoming 2008 YCC tree, so we will have to wait for it to be included in the official scientific NRY YCC tree.
At this time, Ethnoancestry is not sure whether S57 is directly equivalent to the primary DYS413 deletion - it may have occurred either earlier or later. This means that there is a chance that either:
1) Some DYS 413 >18 haplotypes are S57+, (with all DYS 413 <18 haplotypes being S57+) OR
2) Some DYS 413 <18 haplotypes are S57- . (with all DYS 413 >18 haplotypes being S57-)
(If the DYS 413 deletion and S57 are directly equivalent : All DYS 413 >18 haplotypes are S57- and all DYS 413 <18 haplotypes are S57+)
If hypothesis 1) is correct, then most of you in J2a with DYS413 marker results greater than 20 will be negative for S57, but some will be positive (therefore you may like to test for this marker) .
If hypothesis 2) is correct, then most of you in J2a with DYS 413 marker results lower than 19 will be positive for S57, but some will be negative. The project hypothesizes that those of you who fit into either J2a-Alpha or J2a-Beta (or any of the clusters nested within these), will be positive for S57+. The project also hypothesizes that some of you who do not fit in either J2a-Alpha or J2a-Beta cluster* may test negative for S57 (therefore you may like to test for this marker).
Who should test for S57?
Anyone who is confirmed or predicted as J2a (M410) might like to test for this marker, - especially those of you who either have DYS values of 20 or more, or those of you who do not fall into either J2a-Alpha cluster or J2a-Beta cluster*
Those of you who are in J2a-Alpha or J2a-Beta cluster (or any of the clusters nested within these) are probably all positive for this marker (but some of you might like to test anyway to confirm this hypothesis)
Those in J2b (tested or predicted as M12+) will all be negative for this new marker.
[*Please note: For most members in J2a, The first 37 FTDNA markers (or more) are needed to place a haplotype in cluster. If you are not placed in either J2a-Alpha or J2a-Beta (nor any of the clusters nested within these), but do not have all of the first 37 FTDNA markers, then it is likely that having more markers tested will place you within either J2a-Alpha or J2a-Beta] |
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In the October 2007 update we stated that one member in the J2b-Zita cluster received DYS 413 values of 18,23. It was these results which first prompted us to review the validity of DYS 413 as a taxonomic character for the NRY YCC tree. We now have a second member who has tested for DYS 413 who has received the more "normal" results of 21 23. The two members have a genetic distance of 18 at 37 markers (their common ancestor perhaps lived around 3000 years ago, depending on mutation rates).
We can now be confident that this secondary DYS 413 deletion is not characteristic of the whole of J2a-Zita, but it may still be characteristic of a sub-group of J2b-Zita. We still think it is possible that a result of 18 23 may be found in individuals whom are more closely related to the member who received a result of 18 23. |
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We had planned to add some more educational pages to the site at this update, however this will now have to wait until after the next network diagram update. The next network diagram update will be done after the new YCC NRY phylogenetic tree is published. |
- 17 October 2007««
Part one of the October 2007 update
• A new network diagram analysis has been done, adding 38 additional haplotypes. The positions of some of the clusters have altered as a result of these new additions. Part way through the analysis we changed the program which we use to do analyses. Therefore you will see that some of the diagrams are "Network diagrams" created by the program "Network", and some of them are "Phenograms" created with the program "Splits tree". In future analyses we intend to use the program "Splits tree" exclusively, - as it is probably the more appropriate program to use.
• Angela Cone (one of the project admins) has prepared a series of educational pages that help explain about nomenclature and taxonomy. Angela wrote these educational pages because she has had professional expertise in Evolutionary Ecology (including Taxonomy of Plants and Insects).
She has also written a review on the validity of using DYS 413 as a taxonomic character in the YCC NRY phylogenetic tree. We have hinted on several occasions over the past few months that one of our members in the J2b-Zita cluster had "unusual results". This member has DYS 413 values of 18 23. Before we made this public, we wanted to get a clearer idea on how this result might affect the validity of DYS 413 as a taxonomic character in the NRY Phylogenetic tree, and therefore whether this would impact on the validity of the Sengupta et al. 2006 nomenclature. While preparing this report, she discovered that this was definitely not an isolated occurrance. It appears that multirepeat deletions have occurred within the NRY tree on at least 6 different occasions. In four of these instances, a multi-repeat deletion has only been seen on one of the two DYS 413 copies. The full DYS 413 deletion is not unique to J2 M410 haplotypes, - DYS 413 values of 17 17 appear to be found in haplogroup O. In her judgement, it is not valid to use DYS 413 as a character in the YCC tree. Her reasons are fully explained in the pages she has prepared.
To find out the full details, read these pages:
• J2 Nomenclature page
• The DYS 413 review page
• Menu for the taxonomy pages
• Taxonomy basics
• YCC Nomenclature
• Cladistics
The project also notes on the J2 nomenclature page that there is a chance that it might be more valid to call M12+ J2a and M410+ J2b (rather the reverse).
The project will soon see whether the experts agree - there are rumours that a new Y-DNA tree will be presented by Dr Mike Hammer at the next FTDNA conference (20-21 October). We do not have any idea of what changes may have been made to the J portion of the tree (if any). Whatever these changes are, - the J2 Y-DNA project will use that new nomenclature (even if we have to swap J2a & J2b, or call J2 something like I2b or K2 instead).
Part Two of the October 2007 update:
• This will be ready in late October/early November.
• It will contain:
• Updates on: J2b-Zita cluster and J2b-Delta cluster; J2a-Beta cluster and J2a-Gamma cluster.
& ......... a few other interesting observations.
• Updates to the nomenclature used on project pages.
• The new public results page (with the haplotypes of all members that have given us their consent).
• The "members map" will be updated (!!)
- 29 April 2007««
• A new network diagram analysis has been done, adding 28 additional haplotypes . For the 37 marker analysis, seperate analyses for J2a and J2b haplotypes are now done.
• An update to our hypotheses on J2b-Delta -> link <- has been added.
• Our initial review of the Cruciani et al. 2007 paper -> link <- has been added.
• We have added some useful new pages to the site:
• A "frequently asked questions" page. -> link <-
• A page that outlines the scientific method -> link <-
• A page that outlines which clusters appear to be correlated with Jewish ancestry -> link <-
• You may notice that the project now refers to J2-M12+ as J2b (old J2e), and J2 M12-/M410+ as J2a (old J2(xJ2e)), but refers to all sub-clades within each of these clades by their SNP number rather than the sub-clade nomenclature used by Sengupta et al. 2006. For example, we refer to the YCC/FTDNA J2f as J2a-M67+, rather than J2a1b. At the time of the next project analysis update, we will explain indepth our rationale for using the nomenclature in this way.
• In the next few months we hope to begin updating the second phase analysis, and when that is completed we will then revise the third phase analysis. After that is completed, we hope the project will have sufficient data to conclusively answer the projects initial research question. ("Can STR results be used to reliably predict sub-clade in haplogroup J2")
The timeframe in which we will produce these conclusions will depend on how much "free time" we have over the next several months. In the interim, we can say that preliminary results show that several of the markers in the FTDNA 38-67 marker panel are very useful in helping distinguish between subclades. Some of the most salient observations are: |
• There are several markers that are very helpful in distinguishing between J2a and J2b. If a haplotype has YCAII values of 19,20 combined with DYS 578 values of 8, it is almost certain that the haplotype is a J2b one. To date all J2b's have a DYS 578 value of 8, and almost all J2a's have a DYS 578 value of 7 (there is only one known exception).
• It will have been noticed that in J2a, there is one group of J2a M67- haplotypes that cluster together (J2a-Beta in our analysis) and can very easily be distinguished from J2a M67+. On the other hand, there are other J2a M67- haplotypes that cluster together with J2a M67+ haplotypes. To date there is only one marker that we have found that distinguishes between M67+ and M67- with almost 100% accuracy. This marker is DYS 395s1a and to date, all Y-chomosomes that are J2a M67+ have DYS 395s1a values of 15, 15; and almost all J2a M67- haplotypes have marker values that are not 15,15. Most J2a M67- haplotypes have DYS 395s1a values of 14,15, but there is one J2a M67- haplotype that is known to have values of 15,15, one J2a M67- haplotype with DYS 395s1a values of 15, 16, one with DYS 395s1a values of 16,16, and two with DYS 395s1a values of 14,14.
It will be interesting in future to know whether there are additional J2a M67- haplotypes with DYS 395s1a values of 15,15 and if so, whether these have 15,15 values due to convergence or whether these hapotypes are phylogenetically closely related to J2a M67+ haplotypes.
• There are also several marker values that distinguish J2a-Beta from the rest of J2a M67-. However it should be remembered that scientific testing has not yet conclusively confirmed that J2a-Beta does constitute a true phylogenetic grouping (remember cluster ≠ clade). At present it is still a hypothesis that needs to be verified with future SNP discoveries. At present, J2a-Beta is defined solely by STR marker values - so in a way it should be no surprise that there are some marker values that are strongly correlated to J2a-Beta (since that is how J2a-Beta is defined). Using that fact to conclude that J2-Beta is definitely a true monophyletic clade would be an example of circular logic (which is to be avoided in science). Having said that, one marker that appears to conclusively identify membership witin J2a-Beta is DYS 450. All members who have tested for 67 markers and are within J2a-Beta have DYS 450 values of 9. Another marker with characteristic values within J2a-Beta is DYS 445. Within J2a-Lambda (which we hypothesize is a phylogenetic subgrouping within J2a-Beta) the haplotypes which have been tested for DYS 445 have values of 6. Members within J2a-Beta that are not within J2a-Lambda appear to have DYS 445 values of 10. Most other haplotypes within J2a have values of 12, and those within J2b generally have repeat values of 11.
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